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Nickel in PDB 4x5t: Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic

Protein crystallography data

The structure of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic, PDB code: 4x5t was solved by L.Sauguet, P.J.Corringer, C.Huon, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.894, 132.304, 190.517, 90.00, 90.00, 90.00
R / Rfree (%) 25.4 / 27

Other elements in 4x5t:

The structure of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic (pdb code 4x5t). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic, PDB code: 4x5t:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4x5t

Go back to Nickel Binding Sites List in 4x5t
Nickel binding site 1 out of 6 in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:0.9
occ:1.00
OD1 A:ASP88 2.9 0.6 1.0
OD1 A:ASP86 2.9 0.1 1.0
CG A:ASP88 3.5 0.3 1.0
O A:ALA87 3.5 0.1 1.0
OD2 A:ASP88 3.7 0.4 1.0
CG A:ASP86 4.1 0.4 1.0
C A:ALA87 4.2 0.4 1.0
OD2 A:ASP86 4.6 0.9 1.0
CB A:ASP88 4.6 0.1 1.0
N A:ALA87 4.6 0.9 1.0
N A:ASP88 4.7 0.6 1.0
CA A:ASP88 4.8 0.4 1.0
CA A:ALA87 5.0 0.7 1.0

Nickel binding site 2 out of 6 in 4x5t

Go back to Nickel Binding Sites List in 4x5t
Nickel binding site 2 out of 6 in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:0.7
occ:1.00
OD1 B:ASP86 2.9 0.3 1.0
OD1 B:ASP88 3.0 0.1 1.0
O B:ALA87 3.4 0.6 1.0
CG B:ASP88 3.5 0.4 1.0
OD2 B:ASP88 3.7 0.8 1.0
CG B:ASP86 4.1 0.9 1.0
C B:ALA87 4.2 0.6 1.0
OD2 B:ASP86 4.5 0.4 1.0
CB B:ASP88 4.6 0.6 1.0
N B:ALA87 4.7 0.5 1.0
N B:ASP88 4.7 0.3 1.0
CA B:ASP88 4.8 0.3 1.0

Nickel binding site 3 out of 6 in 4x5t

Go back to Nickel Binding Sites List in 4x5t
Nickel binding site 3 out of 6 in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni501

b:0.0
occ:1.00
OD1 C:ASP86 2.6 1.0 1.0
OD1 C:ASP88 3.0 0.4 1.0
O C:ALA87 3.5 0.9 1.0
CG C:ASP88 3.5 0.0 1.0
OD2 C:ASP88 3.7 0.5 1.0
CG C:ASP86 3.8 0.3 1.0
C C:ALA87 4.1 0.3 1.0
OD2 C:ASP86 4.3 0.5 1.0
N C:ALA87 4.4 0.7 1.0
CB C:ASP88 4.6 0.6 1.0
N C:ASP88 4.7 0.4 1.0
C C:ASP86 4.7 0.1 1.0
CA C:ALA87 4.8 0.7 1.0
CA C:ASP88 4.8 0.1 1.0
CB C:ASP86 5.0 0.0 1.0

Nickel binding site 4 out of 6 in 4x5t

Go back to Nickel Binding Sites List in 4x5t
Nickel binding site 4 out of 6 in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni501

b:0.7
occ:1.00
O D:PRO74 3.2 0.0 1.0
NH2 D:ARG85 3.4 95.2 1.0
N D:ILE76 3.7 0.2 1.0
O D:ILE76 4.2 97.3 1.0
CG2 D:ILE73 4.2 0.5 1.0
C D:PRO74 4.3 0.3 1.0
CA D:GLU75 4.3 0.8 1.0
OH D:TYR102 4.4 0.2 1.0
CB D:ILE76 4.4 97.2 1.0
OE1 D:GLU104 4.5 98.0 1.0
C D:GLU75 4.6 0.0 1.0
CA D:ILE76 4.6 99.2 1.0
CD1 D:LEU45 4.6 97.6 1.0
CG1 D:ILE76 4.6 99.3 1.0
CZ D:ARG85 4.7 94.7 1.0
N D:GLU75 4.8 0.4 1.0
CZ D:TYR102 4.8 0.5 1.0
C D:ILE76 4.9 98.1 1.0

Nickel binding site 5 out of 6 in 4x5t

Go back to Nickel Binding Sites List in 4x5t
Nickel binding site 5 out of 6 in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni502

b:0.7
occ:1.00
OD1 D:ASP86 2.6 0.7 1.0
OD1 D:ASP88 2.8 0.6 1.0
CG D:ASP88 3.3 0.7 1.0
OD2 D:ASP88 3.4 0.8 1.0
O D:ALA87 3.6 0.3 1.0
CG D:ASP86 3.7 0.1 1.0
C D:ALA87 4.1 0.0 1.0
OD2 D:ASP86 4.2 0.6 1.0
N D:ALA87 4.5 0.9 1.0
CB D:ASP88 4.5 0.8 1.0
N D:ASP88 4.7 0.3 1.0
C D:ASP86 4.7 0.4 1.0
CA D:ASP88 4.8 0.7 1.0
CA D:ALA87 4.9 0.1 1.0
CB D:ASP86 4.9 0.6 1.0

Nickel binding site 6 out of 6 in 4x5t

Go back to Nickel Binding Sites List in 4x5t
Nickel binding site 6 out of 6 in the Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Alpha 1 Glycine Receptor Transmembrane Structure Fused to the Extracellular Domain of Glic within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni501

b:0.5
occ:1.00
OD1 E:ASP86 2.9 0.3 1.0
OD1 E:ASP88 3.2 0.4 1.0
O E:ALA87 3.3 0.9 1.0
CG E:ASP88 3.6 0.1 1.0
OD2 E:ASP88 3.9 0.6 1.0
C E:ALA87 4.1 0.9 1.0
CG E:ASP86 4.1 0.2 1.0
N E:ALA87 4.5 0.0 1.0
OD2 E:ASP86 4.6 0.9 1.0
CB E:ASP88 4.6 0.2 1.0
N E:ASP88 4.6 0.3 1.0
CA E:ASP88 4.7 0.2 1.0
CA E:ALA87 4.9 0.4 1.0
C E:ASP86 5.0 0.4 1.0

Reference:

G.Moraga-Cid, L.Sauguet, C.Huon, L.Malherbe, C.Girard-Blanc, S.Petres, S.Murail, A.Taly, M.Baaden, M.Delarue, P.J.Corringer. Allosteric and Hyperekplexic Mutant Phenotypes Investigated on An Alpha 1 Glycine Receptor Transmembrane Structure Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1417864112
Page generated: Wed Dec 16 01:37:43 2020

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